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  • cuffnorm_XS_attribute_Error

    Hello,

    I have single end RNA-seq data downloaded from SRA. This RNAseq data lacks XS tag. I manually inserted XS tag by bamutils tool.

    After adding XS tags, I still get the following lines:

    Warning: Your version of Cufflinks is not up-to-date. It is recommended that you ecent features and bug fixes (http://cufflinks.cbcb.umd.edu).
    [20:17:43] Loading reference annotation.
    [20:17:50] Inspecting maps and determining fragment length distributions.
    BAM record error: found spliced alignment without XS attribute
    BAM record error: found spliced alignment without XS attribute

    How could I solve the problem about "BAM record error..." ?

    cufflinks version is 2.2.0.
    Last edited by woker; 06-03-2014, 05:48 AM.

  • #2
    I suggest extract reads from the BAM file and run the whole pipeline. Or use this trick:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

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